Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of MCF-7 cell lines stably overexpressing constitutively active Raf-1, constitutively active MEK, constitutively active c-erbB-2, or ligand-activatable EGFR as models of overexpressed growth factor signaling

ABSTRACT: Profiling of MCF-7 cell lines stably overexpressing constitutively active Raf-1, constitutively active MEK, constitutively active c-erbB-2, or ligand-activatable EGFR as models of overexpressed growth factor signaling, as well as control vector transfected cells (coMCF-7) and control vector transfected cells long-term adapted for estrogen-independent growth (coMCF-7/lt-E2). Experiment Overall Design: Cell lines were profiled in biological triplicates, 18 arrays in all.

ORGANISM(S): Homo sapiens

SUBMITTER: Chad Creighton

PROVIDER: E-GEOD-3542 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Activation of mitogen-activated protein kinase in estrogen receptor alpha-positive breast cancer cells in vitro induces an in vivo molecular phenotype of estrogen receptor alpha-negative human breast tumors.

Creighton Chad J CJ Hilger Amy M AM Murthy Shalini S Rae James M JM Chinnaiyan Arul M AM El-Ashry Dorraya D

Cancer research 20060401 7

Breast cancer presents as either estrogen receptor alpha (ERalpha) positive or negative, with ERalpha+ tumors responding to antiestrogen therapy and having a better prognosis. By themselves, mRNA expression signatures of estrogen regulation in ERalpha+ breast cancer cells do not account for the vast molecular differences observed between ERalpha+ and ERalpha- cancers. In ERalpha- tumors, overexpression of epidermal growth factor receptor (EGFR) or c-erbB-2, leading to increased growth factor sig ...[more]

PMID: 16585219

Similar Datasets

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived constitutively active RhoC mutant (Q63E) overexpressed bladder cancer cells (T24) transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Bladder cancer cells mRNA profiles of vector(VEC) and RhoC constitutively active mutant (Q63E) stably expressing T24 cells were generated by deep sequencing, in triplicate, using Illumina HiSeqX Ten. The sequence reads that passed quality filters were analyzed at the transcript isoform level with the method: Hisat2 2.1.0 followed by StringTie. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the hunam reference genome and identified 209,506 transcripts in the vector(VEC) and constitutively active RhoC mutant (Q63E) transduced bladder cancer cells (T24 cells) with Hisat2 2.1.0 workflow. RNA-seq data confirmed stable expression of known housekeeping genes. Approximately 3% of the transcripts showed differential expression between the vector(VEC) and constitutively active RhoC mutant (Q63E) transduced bladder cancer cells (T24 cells), with a fold change ≥1.5 and p value <0.05. Altered expression of 13 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to RhoC function in bladder cancer. Data analysis with Hisat2 2.1.0 workflow revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of constitutively active RhoC mutant (Q63E) overexpressed bladder cancer cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell line. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

Dataset Information

Transcription profiling of MCF-7 cell lines stably overexpressing constitutively active Raf-1, constitutively active MEK, constitutively active c-erbB-2, or ligand-activatable EGFR as models of overexpressed growth factor signaling

Publications

Activation of mitogen-activated protein kinase in estrogen receptor alpha-positive breast cancer cells in vitro induces an in vivo molecular phenotype of estrogen receptor alpha-negative human breast tumors.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure